Mercurial > repos > rnateam > graphclust_nspdk
diff NSPDK_candidateClusters.xml @ 4:0625db6b6e45 draft
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
| author | rnateam |
|---|---|
| date | Mon, 13 Mar 2017 18:05:04 -0400 |
| parents | ee828c452161 |
| children | 9b5fb987a484 |
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--- a/NSPDK_candidateClusters.xml Mon Feb 27 12:03:12 2017 -0500 +++ b/NSPDK_candidateClusters.xml Mon Mar 13 18:05:04 2017 -0400 @@ -1,113 +1,123 @@ <tool id="NSPDK_candidateClust" name="NSPDK_candidateClusters" version="9.2"> - <requirements> - <requirement type="package" version="0.1.8">graphclust-wrappers</requirement> - <requirement type="package" version="0.5">perl-array-utils</requirement> - <requirement type="package" version="9.2">nspdk</requirement> - </requirements> - <stdio> - <exit_code range="1:" /> - </stdio> - <command> - <![CDATA[ + <requirements> + <requirement type="package" version="0.1.10">graphclust-wrappers</requirement> + <requirement type="package" version="0.5">perl-array-utils</requirement> + <requirement type="package" version="9.2">nspdk</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command> + <![CDATA[ - mkdir -p SVECTOR && - - cp $data_svector SVECTOR/data.svector && - - 'NSPDK_candidateClusters.pl' '$data_fasta' '$data_names' $noCache $ensf $oc $usn $knn $nhf $nspdk_nhf_max $nspdk_nhf_step $GLOBAL_num_clusters $max_rad $max_dist_relations + mkdir ./SVECTOR && - #if $iteration_num.iteration_num_selector: - $iteration_num.CI - '$blacklist' - '$final_partition_soft' - '$fast_cluster_last_round' - $iteration_num.GLOBAL_hit_blacklist_overlap + #for $ins in $data_svector: + ln -f -s '$ins' ./SVECTOR/ && + #end for - #else: - 1 - - #end if + NSPDK_candidateClusters.pl + '$data_fasta' + '$data_names' + $noCache + $ensf + $oc + $usn + $knn + $nhf + $nspdk_nhf_max + $nspdk_nhf_step + $GLOBAL_num_clusters + $max_rad + $max_dist_relations -]]> - </command> - <inputs> - <param type="data" name="data_svector" format="zip" /> - <param type="data" name="data_fasta" format="fasta" /> - <param type="data" name="data_names" format="txt" /> - <conditional name="iteration_num"> - <param name="iteration_num_selector" type="boolean" checked="no" label="Multiple iterations" help="for single iteration- NO, for multiple-YES"/> - <when value="true"> - <param name="CI" type="integer" value="2" size="5" label="Number of current iteration "/> - <param type="data" name="blacklist" format="txt" /> - <param type="data" name="final_partition_soft" format="txt" /> - <param type="data" name="fast_cluster_last_round" format="txt" /> - <param name="GLOBAL_hit_blacklist_overlap" type="float" value="0.2" size="5" label="Blacklist hit overlap" /> - </when> - <when value="false" > - <param name="CI" type="hidden" value="1" size="5" label="Number of current iteration "></param> - </when> - </conditional> - <param name="max_rad" type="integer" value="3" size="5" label="maximum radius " help="-R"/> - <param name="max_dist_relations" type="integer" value="3" size="5" label="maximum distance relations" help="-D"/> - <param name="noCache" truevalue="-no-cache" falsevalue="" checked="True" type="boolean" + #if $iteration_num.iteration_num_selector: + $iteration_num.CI + '$blacklist' + '$final_partition_soft' + '$fast_cluster_last_round' + $iteration_num.GLOBAL_hit_blacklist_overlap + #end if + ]]> + </command> + <inputs> + <param type="data" name="data_svector" multiple="True"/> + <param type="data" name="data_fasta" format="fasta" /> + <param type="data" name="data_names" format="txt" /> + <conditional name="iteration_num"> + <param name="iteration_num_selector" type="boolean" checked="no" label="Multiple iterations" help="for single iteration- NO, for multiple-YES"/> + <when value="true"> + <param name="CI" type="integer" value="2" size="5" label="Number of current iteration "/> + <param type="data" name="blacklist" format="txt" /> + <param type="data" name="final_partition_soft" format="txt" /> + <param type="data" name="fast_cluster_last_round" format="txt" /> + <param name="GLOBAL_hit_blacklist_overlap" type="float" value="0.2" size="5" label="Blacklist hit overlap" /> + </when> + <when value="false" > + <param name="CI" type="hidden" value="1" size="5" label="Number of current iteration "></param> + </when> + </conditional> + <param name="max_rad" type="integer" value="3" size="5" label="maximum radius " help="-R"/> + <param name="max_dist_relations" type="integer" value="3" size="5" label="maximum distance relations" help="-D"/> + <param name="noCache" truevalue="-no-cache" falsevalue="" checked="True" type="boolean" label="Deactivate caching of kernel value computation (-no-cache)" help="to minimize memory usage"/> - <param name="ensf" type="integer" value="5" size="5" label="eccess neighbour size factor" help="-ensf"/> - <param name="usn" truevalue="-usn" falsevalue="" checked="True" type="boolean" + <param name="ensf" type="integer" value="5" size="5" label="eccess neighbour size factor" help="-ensf"/> + <param name="usn" truevalue="-usn" falsevalue="" checked="True" type="boolean" label="Use shared neighbourhood to weight center density (-usn)" help="by default true"/> - <param name="oc" truevalue="-oc" falsevalue="" checked="True" type="boolean" + <param name="oc" truevalue="-oc" falsevalue="" checked="True" type="boolean" label=" flag to output clusters (-oc)" help="by default true"/> - <param name="knn" type="integer" value="20" size="5" label="Number of nearest neighbors" help="-knn num"/> - <param name="nhf" type="integer" value="500" size="5" label="Number of hash functions " help="-nhf num"/> - <param name="nspdk_nhf_max" type="integer" value="1000" size="5" label="Maximal number of hash functions " /> - <param name="nspdk_nhf_step" type="integer" value="25" size="5" label="Size of step for increasing hash functions " help="The number of hash functions is increased by this value after each iteration."/> - <param name="GLOBAL_num_clusters" type="integer" value="100" size="5" label="Maxinum number of clusters " /> - </inputs> - <outputs> - <data name="fast_cluster" format="txt" from_work_dir="SVECTOR/data.svector.1.fast_cluster" label="fast_cluster.1" > - <filter> iteration_num['iteration_num_selector'] is False</filter> - </data> - <data name="fast_cluster_sim" format="txt" from_work_dir="SVECTOR/data.svector.1.fast_cluster_sim" label="fast_cluster_sim.1" > - <filter> iteration_num['iteration_num_selector'] is False </filter> - </data> - <data name="black_list" format="txt" from_work_dir="SVECTOR/data.svector.blacklist.1" label="blacklist.1" > - <filter> iteration_num['iteration_num_selector'] is False </filter> - </data> - <data name="fast_cluster_m" format="txt" from_work_dir="SVECTOR/data.svector.*.fast_cluster" label="fast_cluster.$iteration_num.CI" > - <filter> iteration_num['iteration_num_selector'] is True</filter> - </data> - <data name="fast_cluster_sim_m" format="txt" from_work_dir="SVECTOR/data.svector.*.fast_cluster_sim" label="fast_cluster_sim.$iteration_num.CI" > - <filter> iteration_num['iteration_num_selector'] is True</filter> - </data> - <data name="black_list_m" format="txt" from_work_dir="SVECTOR/data.svector.blacklist.*" label="blacklist.$iteration_num.CI" > - <filter> iteration_num['iteration_num_selector'] is True</filter> - </data> - </outputs> - <tests> - <test> - <param name="data_fasta" value="data.fasta"/> - <param name="data_names" value="data.names"/> - <param name="data_svector" value="data.svector.1" ftype="zip" /> - <conditional name="iteration_num"> - <param name="iteration_num_selector" value="false"/> - </conditional> - <param name="noCache" value="-no-cache"/> - <param name="ensf" value="5"/> - <param name="oc" value="-oc"/> - <param name="max_rad" value="3"/> - <param name="max_dist_relations" value="3"/> - <param name="usn" value="-usn"/> - <param name="knn" value="20"/> - <param name="nhf" value="500"/> - <param name="nspdk_nhf_max" value="1000"/> - <param name="nspdk_nhf_step" value="25"/> - <param name="GLOBAL_num_clusters" value="100"/> - <output name="fast_cluster" file="SVECTOR/data.svector.1.fast_cluster" /> - <output name="fast_cluster_sim" file="SVECTOR/data.svector.1.fast_cluster_sim" /> - <output name="black_list" file="SVECTOR/data.svector.blacklist.1" /> - </test> - </tests> - <help> - <![CDATA[ + <param name="knn" type="integer" value="20" size="5" label="Number of nearest neighbors" help="-knn num"/> + <param name="nhf" type="integer" value="500" size="5" label="Number of hash functions " help="-nhf num"/> + <param name="nspdk_nhf_max" type="integer" value="1000" size="5" label="Maximal number of hash functions " /> + <param name="nspdk_nhf_step" type="integer" value="25" size="5" label="Size of step for increasing hash functions " help="The number of hash functions is increased by this value after each iteration."/> + <param name="GLOBAL_num_clusters" type="integer" value="100" size="5" label="Maxinum number of clusters " /> + </inputs> + <outputs> + <data name="fast_cluster" format="txt" from_work_dir="SVECTOR/data.svector.1.fast_cluster" label="fast_cluster.1" > + <filter> iteration_num['iteration_num_selector'] is False</filter> + </data> + <data name="fast_cluster_sim" format="txt" from_work_dir="SVECTOR/data.svector.1.fast_cluster_sim" label="fast_cluster_sim.1" > + <filter> iteration_num['iteration_num_selector'] is False </filter> + </data> + <data name="black_list" format="txt" from_work_dir="SVECTOR/data.svector.blacklist.1" label="blacklist.1" > + <filter> iteration_num['iteration_num_selector'] is False </filter> + </data> + <data name="fast_cluster_m" format="txt" from_work_dir="SVECTOR/data.svector.*.fast_cluster" label="fast_cluster.$iteration_num.CI" > + <filter> iteration_num['iteration_num_selector'] is True</filter> + </data> + <data name="fast_cluster_sim_m" format="txt" from_work_dir="SVECTOR/data.svector.*.fast_cluster_sim" label="fast_cluster_sim.$iteration_num.CI" > + <filter> iteration_num['iteration_num_selector'] is True</filter> + </data> + <data name="black_list_m" format="txt" from_work_dir="SVECTOR/data.svector.blacklist.*" label="blacklist.$iteration_num.CI" > + <filter> iteration_num['iteration_num_selector'] is True</filter> + </data> + </outputs> + <tests> + <test> + <param name="data_fasta" value="data.fasta"/> + <param name="data_names" value="data.names"/> + <param name="data_svector" value="data.svector.1" ftype="zip" /> + <conditional name="iteration_num"> + <param name="iteration_num_selector" value="false"/> + </conditional> + <param name="noCache" value="-no-cache"/> + <param name="ensf" value="5"/> + <param name="oc" value="-oc"/> + <param name="max_rad" value="3"/> + <param name="max_dist_relations" value="3"/> + <param name="usn" value="-usn"/> + <param name="knn" value="20"/> + <param name="nhf" value="500"/> + <param name="nspdk_nhf_max" value="1000"/> + <param name="nspdk_nhf_step" value="25"/> + <param name="GLOBAL_num_clusters" value="100"/> + <output name="fast_cluster" file="SVECTOR/data.svector.1.fast_cluster" /> + <output name="fast_cluster_sim" file="SVECTOR/data.svector.1.fast_cluster_sim" /> + <output name="black_list" file="SVECTOR/data.svector.blacklist.1" /> + </test> + </tests> + <help> + <![CDATA[ **What it does** @@ -133,10 +143,10 @@ ]]> - </help> - <citations> - <citation type="doi">10.1093/bioinformatics/bts224</citation> - <citation type="bibtex">@inproceedings{costa2010fast, + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/bts224</citation> + <citation type="bibtex">@inproceedings{costa2010fast, title={Fast neighborhood subgraph pairwise distance kernel}, author={Costa, Fabrizio and De Grave, Kurt}, booktitle={Proceedings of the 26th International Conference on Machine Learning}, @@ -145,5 +155,5 @@ organization={Omnipress} } </citation> - </citations> + </citations> </tool>